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Finding themselves face to face with a mysterious middle aged gentleman who greets them with French, Ruby and Sapphire quickly inquires who he is, where they are, and what has happened to the great turmoil in Hoenn. The man frowns and says they must wait til a question is answered before asking another, and to Ruby and Sapphire's surprise, addresses them by their names.

The gentleman introduces himself as Juan, the teacher of Wallace, and says he has come back to take up the Sootopolis gym again due to Wallace's request. Ruby gasps with shock that the man standing in front of him is the teacher of his own teacher, and is even more surprised that Wallace is giving up his position as a gymleader.

Juan then reveals that they are currently on the Mirage Island, a mysterious solitary islet in Hoenn that is essentially separated from the rest of the region, which real name is not known of but is given many different callings. While Sapphire thinks hard to recall if she has heard of such a place before, Juan proceeds to answer their third question. He retrieves a greatball from his sleeve to send out his Kingdra, who then spurts out a shower of water to create an aqua screen.

To Ruby and Sapphire's surprise, the ongoing battle between Groudon and Kyogre gradually appears on the screen, and Juan states that it is the latest happenings in Sootopolis. Ruby and Sapphire couldn't understand why the two titans are still fighting, and Juan explains that their plan to stop the creatures' rampaging by knocking out the Red and Blue Orbs from Team Magma and Team Aqua's leaders didn't work out the way they hoped.

After they lent the Grand Meteor's powers to blast out the orbs from Archie and Maxie, they indeed managed to stop Kyogre and Groudon momentarily. However, it failed to calm them. Instead, since the two titans have been unleashing their full powers since the beginning of the battle, they have cultivated a massive amount of energy in the city. When they were abruptly freed from the restraints from the Red and Blue Orbs, they started to lose control of themselves, and rampaged even more savagely.

What's worse is that their momentary halt in action actually caused the stored energies to condense rapidly, leading to a series of energy explosions which is now expanding out from Sootopolis to every direction. In fact, the powerful waves were about to consume Ruby and Sapphire when Juan saved them just in time and took them to the Mirage Island.

Juan remarks that perhaps their land's current situation is the catastrophy that is said to befall Hoenn if the ancient titans are awakened. However, he tells Ruby and Sapphire not to worry too much, as there are powerful and devoted people who are working hard to hold back the destructive energies from expanding out of Sootopolis.

Sapphire wonders how it is possible, and Juan grins that they are using superpower, the signature attack of Hoenn's top class forces, Regirock, Regice and Registeel, and the six trainers controlling these three legendaries golems are no other than the old and new Champions, Steven and Wallace, as well as the Hoenn Elite 4, Sidney, Drake, Phoebe and Glacia.

Juan adds that it was all thanks to Sapphire who helped awaken the three creatures, and says it was certainly more than coincidence. Ruby gets confused after hearing Juan address Steven and Wallace as the old and new champion, and Juan is surprised that Ruby doesn't know Steven has passed the champion title back to Wallace after the young man has apparently forseen something in the battle.

Juan then stops Ruby and Sapphire from asking further questions, and says everything else doesn't matter at the moment. He puts on a seriously tone, and states that what Steven, Wallace and the Elite 4 are doing could actually achieve nothing but to stall time, and the job to put a stop to Kyogre and Groudon lies in the hands of Ruby and Sapphire, which is why they must not waste more time and should start on their special training immediately.

He beckons the young boy and young girl behind him whom he addresses as Tate and Liza, and the two without warning order a combined extrasensory from their two Spoinks. Taken by surprise, Ruby and Sapphire jump out of the way just in time, and quickly send out their Castform, Popo, and Lairon, Ronono, to fight.

Sapphire demands to know what Juan is doing, but Ruby stops her, and begins his usual speech of introducing Popo during contests. Stating that it is the Pokémon whose talent shines under any weather condition, Ruby orders a weatherball, and Popo swiftly delivers a shimmering blast towards Juan.

But Juan is prepared as well. Twirling his body in a graceful move, he commands a waterpulse from Kindgra, and the attack collides with Popo's weatherball, creating a shower of rain. Astounded by the skills and elegance of Juan, Ruby is more than convinced that the man is really the teacher of Wallace. Addressing Juan as his great teacher, Ruby says while he still hasn't fully digested all the latest happenings around him, he is grateful that they could play a role in stopping Groudon and Kyogre, and agrees to accept the special training the man offers.

Juan compliments Ruby's attitude with the French word tres bien, and grins that Wallace has got himself a nice student. He remarks that they really are running out of time, and motions Ruby and Sapphire to pick up the Pokédexes they have dropped on the ground when they were still unconscious.

He then proceeds to the first topic of his training, which is double battles, and says Tate and Liza shall train them in that aspect. He reveals that the two are actually the gymleaders of the Mossdeep Gym, and while they nearly perished in a fight against Team Magma at Mt. Pyre which he saved them from, the two are highly specialized in double battles and are experts in using combination moves. He wants Ruby and Sapphire to learn as much as possible from them, and says they must make good use of each moment, as time is difficult to follow on the Mirage Island.

Ruby wonders what it means, and Juan realizes that he has not told them the most important thing about the Mirage Island. It turns out that the way time flows on the island is different from the rest of the world. Ruby and Sapphire have been unconscious on the island for 3 days, but during that period, time flowed seven times as fast in the outside world, which means 21 days have actually passed while they were on the island.

The piece of information leaves both Ruby and Sapphire speechless for a moment, and Sapphire refuses to believe such a ridiculous thing. Suddenly, Liza gets an uneasy feeling again, and Juan wonders what is wrong. Tate tells him that Liza has been feeling some unidentified foreign presence on the island since Ruby and Sapphire arrived, and she suspects that some outside Pokémon or trainers are have also come to the island.

Not far away, behind several Liechi Berry plants, the Plusle and Minun who were washed off the abandoned ship by Kyogre peek out from their hiding place while clutching tight to the diary they brought along with them...